Yamal produced another moment of individual brilliance to put Spain ahead in the sixth minute, cutting inside onto his left foot before curling a stunning effort into the top corner.
The goal left De la Fuente with his hands on his head on the touchline, and the Spain boss was once again full of praise for the Barcelona winger after the match.
"Lamine never stops surprising us," De la Fuente said. "He has so much talent and so much quality. He still has a lot to offer us, too, and there is a long way to go until we see the best Lamine."
The 19-year-old has been one of the standout players of the international break, scoring in each of his last three appearances for Spain. He has found the net four times in three matches during the current run, while also scoring inside the opening minutes against both England and Croatia.
His latest contribution helped the world champions maintain their perfect start to their Nations League campaign and remain three points clear of England at the top of Group A3.
De la Fuente believes Yamal's development is far from complete and suggested his performances could eventually earn him legendary status with the national team.
"Lamine is on the path to becoming a legend," he said.
The winger's form has also strengthened his case in the Ballon d'Or discussion, with De la Fuente going as far as to say he would consider Yamal the world's best player if he were Spain's only nominee.
"He does everything well," the coach said. "If he's not the best, then it's because of competition from the other Spanish players, and even then he's one of the best for sure."
Yamal was replaced at half-time with Spain leading 2-0 after Rodri had added a second goal. Without their teenage winger, Spain struggled to maintain the same rhythm after the break.
Czechia pulled one back through Jiri Slama and briefly threatened to make the closing stages uncomfortable before Mikel Merino settled the contest late on. Czechia were also reduced to 10 men after Ladislav Krejci was sent off.
De la Fuente admitted Spain's second-half display fell below the level of their opening 45 minutes, although he was pleased to have protected Yamal and other players after a demanding schedule.
"The first half went very well, but the second didn't," he said. "Four matches in 10 days is tough. Today it was about winning and putting in a good performance, but also about protecting the players."
Spain now face a very different challenge when they travel to Croatia on Tuesday.
Croatia will be looking to respond after suffering a record 7-0 defeat to England, and De la Fuente expects that result to fuel their reaction.
"They'll be suffering from stung pride and have an excess of motivation," he warned.
Spain will therefore attempt to maintain their unbeaten run and preserve their position at the top of the group when they meet Croatia in their final match of the international break.